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macros.xml
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<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.48.0</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="0.4_3">r-snow</requirement>
<requirement type="package" version="1.2.6">bioconductor-genomeinfodbdata</requirement>
<requirement type="package" version="@TOOL_VERSION@">bioconductor-camera</requirement>
<requirement type="package" version="2.48.0">bioconductor-multtest</requirement>
<requirement type="package" version="1.1_5">r-batch</requirement>
<requirement type="package" version="1.3.26">graphicsmagick</requirement>
<requirement type="package" version="3.0">zip</requirement>
</requirements>
</xml>
<xml name="stdio">
<stdio>
<exit_code range="1" level="fatal" />
</stdio>
</xml>
<token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
<!-- raw file load for planemo test -->
<token name="@COMMAND_FILE_LOAD@">
#if $file_load_section.file_load_conditional.file_load_select == "yes":
#if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
#set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
#set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
#else
zipfile '$file_load_section.file_load_conditional.input'
#end if
#end if
</token>
<xml name="input_file_load">
<section name="file_load_section" title="Resubmit your raw dataset or your zip file">
<conditional name="file_load_conditional">
<param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
<option value="no" >no need</option>
<option value="yes" >yes</option>
</param>
<when value="no">
</when>
<when value="yes">
<param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
</when>
</conditional>
</section>
</xml>
<xml name="test_file_load_zip">
<section name="file_load_section">
<conditional name="file_load_conditional">
<param name="file_load_select" value="yes" />
<param name="input" value="faahKO_reduce.zip" ftype="zip" />
</conditional>
</section>
</xml>
<xml name="test_file_load_single">
<section name="file_load_section">
<conditional name="file_load_conditional">
<param name="file_load_select" value="yes" />
<param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
</conditional>
</section>
</xml>
<!-- peaklist export option management -->
<token name="@COMMAND_PEAKLIST@">
convertRTMinute $export.convertRTMinute
numDigitsMZ $export.numDigitsMZ
numDigitsRT $export.numDigitsRT
intval $export.intval
</token>
<xml name="input_peaklist">
<section name="export" title="Export options">
<param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
<param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
<param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
<param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
<option value="into" selected="true">into</option>
<option value="maxo" >maxo</option>
<option value="intb">intb</option>
</param>
</section>
</xml>
<xml name="test_peaklist">
<section name="export">
<param name="convertRTMinute" value="True"/>
<param name="numDigitsMZ" value="4" />
<param name="numDigitsRT" value="1" />
<param name="intval" value="into"/>
</section>
</xml>
<!-- annotate_diffreport <test> commun part -->
<xml name="test_annotate_diffreport">
<section name="groupfwhm">
<param name="sigma" value="6"/>
<param name="perfwhm" value="0.6"/>
</section>
<section name="findisotopes">
<param name="maxcharge" value="3"/>
<param name="maxiso" value="4"/>
<param name="minfrac" value="0.5"/>
</section>
<section name="findgeneral">
<param name="ppm" value="5"/>
<param name="mzabs" value="0.015"/>
<param name="max_peaks" value="100"/>
</section>
<section name="diffreport">
<conditional name="options">
<param name="option" value="show"/>
<param name="eicmax" value="200"/>
<param name="eicwidth" value="200"/>
<param name="value" value="into"/>
<param name="h" value="480"/>
<param name="w" value="640"/>
<param name="mzdec" value="2"/>
<param name="sortpval" value="False"/>
<param name="tabular2" value="zip"/>
<param name="png2" value="zip"/>
</conditional>
</section>
<expand macro="test_peaklist"/>
</xml>
<xml name="test_annotate_quick_false">
<param name="quick" value="FALSE"/>
<section name="groupcorr">
<param name="cor_eic_th" value="0.75"/>
<param name="graphMethod" value="hcs"/>
<param name="pval" value="0.05"/>
<param name="calcCiS" value="True"/>
<param name="calcIso" value="False"/>
<param name="calcCaS" value="False"/>
</section>
</xml>
<xml name="test_annotate_quick_true">
<conditional name="quick_block">
<param name="quick" value="TRUE"/>
</conditional>
</xml>
<token name="@HELP_AUTHORS@">
.. class:: infomark
**Authors** Colin A. Smith [email protected], Ralf Tautenhahn [email protected], Steffen Neumann [email protected], Paul Benton [email protected] and Christopher Conley [email protected]
.. class:: infomark
**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton [email protected] - part of Workflow4Metabolomics.org [W4M]
| Contact [email protected] for any questions or concerns about the Galaxy implementation of this tool.
---------------------------------------------------
</token>
<token name="@HELP_CAMERA_NEWVERSION_1480@">
**Version 2.2.6+camera1.48.0 - 11/06/2021**
- UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
</token>
<token name="@HELP_CAMERA_NEWVERSION_1460@">
**Version 2.2.6+camera1.46.0 - 12/04/2021**
- UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_)
</token>
<token name="@HELP_CAMERA_NEWVERSION_1420@">
**Version 2.2.6+camera1.42.0 - 13/02/2020**
- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 (see CAMERA News_)
</token>
<xml name="citation">
<citations>
<citation type="doi">10.1021/ac202450g</citation>
<citation type="doi">10.1093/bioinformatics/btu813</citation>
</citations>
</xml>
</macros>